WiX VS Project ignores GenerateProjectSpecificOutputFolder MsBuild property, from @Karankang007, points out that the WiX v3.x MSBuild targets do not support the GenerateProjectSpecificOutputFolder property. As GenerateProjectSpecificOutputFolder is part of the common MSBuild targets, WiX v4.x's MSBuild targets automatically get that support but WiX v3.x would need to manually implement it. We took this issue into the v3 backlog if someone wanted to implement this functionality.
This week's update on WiX v3.10.3 is that this is the last update on WiX v3.10.3. WiX v3.10.3 was released on 4-July as planned (in plan v12.3.9). You can download WiX v3.10.3 and read more about the release on my blog and Rob's blog.